The heritable landscape of near-infrared and Raman spectroscopic measurements to improve lipid content in Atlantic salmon fillets

Gareth F Difford,Siri S Horn,Bente Ruyter,Binyam S Dagnachew,Nils K Afseth,Anna K Sonesson,Borghild Hillestad,Katinka R Dankel

doi:10.1186/s12711-021-00605-6

Gareth F Difford, Siri S Horn + Show 6 more

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https://doi.org/10.1186/s12711-021-00605-6

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Abstract

BackgroundProduct quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves. Fillet lipid content is a heritable trait and is unfavourably correlated with growth, thus genetic management of fillet lipid content is needed for sustained genetic progress in these two traits. The laboratory-based reference method for recording fillet lipid content is highly accurate and precise but, at the same time, expensive, time-consuming, and destructive. Here, we test the use of rapid and cheaper vibrational spectroscopy methods, namely near-infrared (NIR) and Raman spectroscopy both as individual phenotypes and phenotypic predictors of lipid content in Atlantic salmon.ResultsRemarkably, 827 of the 1500 individual Raman variables (i.e. Raman shifts) of the Raman spectrum were significantly heritable (heritability (h2) ranging from 0.15 to 0.65). Similarly, 407 of the 2696 NIR spectral landscape variables (i.e. wavelengths) were significantly heritable (h2 = 0.27–0.40). Both Raman and NIR spectral landscapes had significantly heritable regions, which are also informative in spectroscopic predictions of lipid content. Partial least square predicted lipid content using Raman and NIR spectra were highly concordant and highly genetically correlated with the lipid content values ({r}_{text{g}} = 0.91–0.98) obtained with the reference method using Lin’s concordance correlation coefficient (CCC = 0.63–0.90), and were significantly heritable ({h}^{2} = 0.52–0.67).ConclusionsBoth NIR and Raman spectral landscapes show substantial additive genetic variation and are highly genetically correlated with the reference method. These findings lay down the foundation for rapid spectroscopic measurement of lipid content in salmonid breeding programmes.

Highlights

Product quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves
Since growth is the most highly weighted trait in Atlantic salmon breeding programmes [9], selection indices and economic weighting of fillet lipid content are needed to achieve a genetic gain in growth without undesirable correlated responses in fillet lipid content [10], which can have knock-on effects on product quality and production efficiency
827 Raman shifts were significantly heritable at α = 0.05 after correction for a false discovery rate (FDR) of 10%

Summary

Introduction

Product quality and production efficiency of Atlantic salmon are, to a large extent, influenced by the deposition and depletion of lipid reserves. Since growth is the most highly weighted trait in Atlantic salmon breeding programmes [9], selection indices and economic weighting of fillet lipid content are needed to achieve a genetic gain in growth without undesirable correlated responses in fillet lipid content [10], which can have knock-on effects on product quality and production efficiency. As the gold standard or reference method, this method is the most accurate and precise measurement from which all other methods are benchmarked, and it is regarded as providing the ‘True’ value. It is time-consuming, costly, and is classified as a destructive method because both the fish and the fillet are sacrificed in the process. To the best of our knowledge, direct genetic evaluations using the reference method for measurement of fillet lipid have only recently been reported for Atlantic salmon [13]

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